Repositories list

• juicer

  Public
  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

  hi-c3d-genome3d-genome-browser+ 3bioinformaticsgenomicsngs

  Shell

  •

  MIT License

  •190•461•99•8•Updated Aug 31, 2025Aug 31, 2025

• straw

  Public
  Extract data quickly from Juicebox via straw

  C++

  •

  MIT License

  •35•69•32•1•Updated Apr 6, 2025Apr 6, 2025

• juicebox.js

  Public
  HiC contact matrix visualization

  JavaScript

  •

  MIT License

  •14•22•22•0•Updated Mar 18, 2025Mar 18, 2025

• juicebox-web

  Public
  JavaScript

  •1•3•3•0•Updated Mar 18, 2025Mar 18, 2025

• juicebox.js_AL

  Public
  HiC contact matrix visualization

  JavaScript

  •

  MIT License

  •14•0•0•0•Updated Feb 15, 2025Feb 15, 2025

• hic-straw

  Public
  Command line and web utilities for reading .hic contact matrix files

  JavaScript

  •

  MIT License

  •4•10•0•0•Updated Feb 3, 2025Feb 3, 2025

• Juicebox

  Public
  Visualization and analysis software for Hi-C data -

  Java

  •

  MIT License

  •60•271•259•3•Updated Aug 6, 2024Aug 6, 2024

• sw2stl

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Aug 2, 2024Aug 2, 2024

• 3d-carta

  Public
  Shell

  •

  MIT License

  •0•0•0•0•Updated May 22, 2024May 22, 2024

• clear-tools

  Public
  Chromatin Landscape Exploration, Analysis, and Research Tools

  Java

  •

  MIT License

  •2•0•0•0•Updated Apr 26, 2024Apr 26, 2024

• 3d-dna

  Public
  3D de novo assembly (3D DNA) pipeline

  Shell

  •

  MIT License

  •55•216•66•1•Updated Nov 29, 2023Nov 29, 2023

• BEAR

  Public
  BEAR: viral diagnostic analysis pipeline for SARS-CoV-2

  viral-metagenomicscovid-19bioinformatics

  Shell

  •

  MIT License

  •1•6•1•0•Updated Feb 23, 2023Feb 23, 2023

• PAP

  Public
  Shell

  •0•0•0•0•Updated Jan 23, 2023Jan 23, 2023

• EigenVector

  Public
  R functions for very fast eigenvector calculation

  C

  •9•8•0•1•Updated Jan 18, 2023Jan 18, 2023

• HiCTools

  Public
  Java

  •

  MIT License

  •3•10•1•0•Updated Jan 18, 2023Jan 18, 2023

• welcome

  Public
  Getting started with Hi-C data analysis

  HTML

  •

  MIT License

  •0•5•0•0•Updated Dec 4, 2022Dec 4, 2022

• welcome-images

  Public
  0•0•0•0•Updated Dec 4, 2022Dec 4, 2022

• mmba

  Public
  Moshe's matrix balancing algorithm

  C

  •0•0•1•0•Updated Oct 12, 2022Oct 12, 2022

• java-straw

  Public
  Java

  •

  MIT License

  •4•0•0•0•Updated Sep 29, 2022Sep 29, 2022

• JuiceboxGUI

  Public
  Java

  •

  MIT License

  •2•6•1•0•Updated Sep 29, 2022Sep 29, 2022

• hic2gatk

  Public
  Shell

  •

  MIT License

  •1•1•0•0•Updated Sep 28, 2022Sep 28, 2022

• hic-format

  Public
  0•3•0•1•Updated Sep 14, 2022Sep 14, 2022

• pyStraw

  Public
  Python only flavor of straw for streaming .hic data [Deprecated]

  Jupyter Notebook

  •

  MIT License

  •1•3•0•0•Updated Feb 4, 2022Feb 4, 2022

• JuicerTools

  Public
  Java

  •

  MIT License

  •2•16•5•0•Updated Jan 1, 2022Jan 1, 2022

• JuiceboxReader

  Public
  [Deprecated] Fast reading/dump for .hic files

  C++

  •

  MIT License

  •0•0•1•0•Updated Dec 18, 2021Dec 18, 2021

• mcph1_notebook

  Public
  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Dec 13, 2021Dec 13, 2021

• JuiceMe

  Public
  Hi-Culfite Processing Pipeline

  Shell

  •

  MIT License

  •1•3•0•0•Updated Jul 8, 2021Jul 8, 2021

• bwa-meth

  Public
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

  PostScript

  •

  MIT License

  •58•0•0•0•Updated Jun 2, 2021Jun 2, 2021

• contact-probability

  Public
  Updated Adrian's code

  Python

  •0•0•1•0•Updated Feb 27, 2020Feb 27, 2020

• juicer_old

  Public
  Aiden Lab old version of Juicer, for archival purposes

  Python

  •0•0•0•0•Updated Mar 28, 2018Mar 28, 2018